[English] 日本語
Yorodumi
- PDB-5oqk: Solution NMR structure of truncated, human Hv1/VSOP (Voltage-gate... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oqk
TitleSolution NMR structure of truncated, human Hv1/VSOP (Voltage-gated proton channel)
ComponentsVoltage-gated hydrogen channel 1
KeywordsPROTON TRANSPORT / voltage gated proton channel / anti-parallel four-helix bundle / membrane protein
Function / homology
Function and homology information


Sperm Motility And Taxes / voltage-gated proton channel activity / regulation of acrosome reaction / cellular response to pH / voltage-gated monoatomic cation channel activity / ROS and RNS production in phagocytes / regulation of reactive oxygen species biosynthetic process / response to pH / cellular response to zinc ion / monoatomic ion channel complex ...Sperm Motility And Taxes / voltage-gated proton channel activity / regulation of acrosome reaction / cellular response to pH / voltage-gated monoatomic cation channel activity / ROS and RNS production in phagocytes / regulation of reactive oxygen species biosynthetic process / response to pH / cellular response to zinc ion / monoatomic ion channel complex / response to zinc ion / single fertilization / sperm flagellum / specific granule membrane / proton transmembrane transport / positive regulation of superoxide anion generation / secretory granule membrane / cell redox homeostasis / regulation of intracellular pH / phagocytic vesicle membrane / apical plasma membrane / innate immune response / Neutrophil degranulation / protein homodimerization activity / identical protein binding / membrane / plasma membrane
Similarity search - Function
Voltage-gated hydrogen channel 1, C-terminal membrane-localisation domain / Voltage-gated hydrogen channel 1 / C-terminal membrane-localisation domain of ion-channel, VCN1 / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Voltage-gated hydrogen channel 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBayrhuber, M. / Maslennikov, I. / Kwiatowski, W. / Sobol, A. / Wierschem, C. / Eichmann, C. / Riek, R.
CitationJournal: Biochemistry / Year: 2019
Title: Nuclear Magnetic Resonance Solution Structure and Functional Behavior of the Human Proton Channel.
Authors: Bayrhuber, M. / Maslennikov, I. / Kwiatkowski, W. / Sobol, A. / Wierschem, C. / Eichmann, C. / Frey, L. / Riek, R.
History
DepositionAug 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_nmr_spectrometer.model
Revision 1.2Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Voltage-gated hydrogen channel 1


Theoretical massNumber of molelcules
Total (without water)17,3521
Polymers17,3521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11350 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Voltage-gated hydrogen channel 1 / Hydrogen voltage-gated channel 1 / HV1 / Voltage sensor domain-only protein


Mass: 17352.062 Da / Num. of mol.: 1 / Fragment: UNP residues 82-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HVCN1, VSOP, UNQ578/PRO1140 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q96D96

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D HNCA
121isotropic23D HNCO
131isotropic23D HN(CA)CB
141isotropic23D 1H-15N NOESY
151isotropic23D 1H-13C NOESY

-
Sample preparation

DetailsType: micelle
Contents: 0.4 mM [U-99% 13C; U-99% 15N; 50% 2H] Hv1/VSOP, 20 mM MES, 20 mM BisTris, 2 mM FC-12, 2 mM LDAO, 1 mM TCEP, 10 mM ZnCl2, 90% H2O/10% D2O
Label: sample-1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMHv1/VSOP[U-99% 13C; U-99% 15N; 50% 2H]1
20 mMMESnatural abundance1
20 mMBisTrisnatural abundance1
2 mMFC-12natural abundance1
2 mMLDAOnatural abundance1
1 mMTCEPnatural abundance1
10 mMZnCl2natural abundance1
Sample conditionsIonic strength: 30 mM / Label: conditions_1 / pH: 5.8 / Pressure: 1 atm / Temperature: 310 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

-
Processing

NMR softwareName: CYANA / Developer: Guntert P. / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more